Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 258 bits (659), Expect = 2e-73 Identities = 149/366 (40%), Positives = 212/366 (57%), Gaps = 29/366 (7%) Query: 4 IHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRI 63 I + + K Y G + + + +G+ +V+LGPSGCGK+T+LR+IAGLE ++ GT+ I Sbjct: 3 IEIRDVRKDY-GRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHI 61 Query: 64 GGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLN 123 GT V LP +RN++MVFQ+YAL+PH++V +NI FGL+ K PA EI+RR++ V LL Sbjct: 62 AGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLG 121 Query: 124 LEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQR 183 L L+ KP +SGG QQR A+ RAII V L DEPLSNLDAKLR +R +I L +R Sbjct: 122 LSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRR 181 Query: 184 LRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFL 243 L T +YVTHDQ+EAMT+ADR++LM+DG+IVQ SP Y P N F A FIGTP MN + Sbjct: 182 LGITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIV 241 Query: 244 ------SGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPA 297 G G+L + +R+ +RP+++R+A +PA Sbjct: 242 PLCPTQGGAALEPGGRLLFP------GMDPDRY---------LFGIRPENLRLAESGQPA 286 Query: 298 ASLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDV 357 V E LG+D ++ Q + R + G + L D ++++FD Sbjct: 287 -------MVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDA 339 Query: 358 ESGENL 363 + E + Sbjct: 340 RTQERV 345 Lambda K H 0.321 0.137 0.403 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 391 Number of extensions: 15 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 406 Length of database: 365 Length adjustment: 30 Effective length of query: 376 Effective length of database: 335 Effective search space: 125960 Effective search space used: 125960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory